There's only one Sphene we interact with throughout Dawntrail: an AI replica modeled on the living Sphene's memories, modified to prioritize Alexandria's preservation and the happiness of its citizens over all else. There's two layers to her - the memories and the programming - in constant competition throughout Dawntrail until her programming determines that her memories (personality) are detrimental to her purpose and she can't emotionally handle the grief and guilt it entails.

It is heavily implied that Sphene wants to stop but due to her personality and programming is unable to do so, so she names us her executioner and spirits everyone else away because she knows the PC is capable of defeating her. Never stated verbatim, but reading between the lines a little...